Upper respiratory Streptococcus pneumoniae colonization among working-age adults with prevalent exposure to overcrowding

ABSTRACT Most pneumococcal disease occurs among infants and older adults and is thought to be driven by the transmission of Streptococcus pneumoniae from young children to these vulnerable age groups. However, pneumococcal disease outbreaks also affect non-elderly adults living or working in congregate, close-contact settings. Little is known about pneumococcal carriage in such populations. From July to November 2020, we collected saliva from low-income adult farmworkers in Monterey County, California, and tested for pneumococcal carriage following culture enrichment via quantitative PCR assays targeting the pneumococcal lytA and piaB genes. Participants were considered to carry pneumococci if lytA and piaB cycle threshold values were both below 40. Among 1,283 participants enrolled in our study, 117 (9.1%) carried pneumococci. Carriers tended more often than non-carriers to be exposed to children aged <5 years [odds ratio (OR) = 1.45 (0.95–2.20)] and overcrowding [OR = 1.48 (0.96–2.30) and 2.84 (1.20–6.73), respectively, for participants in households with >2–4 and >4 persons per bedroom vs ≤2 persons per bedroom]. Household overcrowding remained associated with increased risk of carriage among participants not exposed to children aged <5 years [OR = 2.05 (1.18–3.59) for participants living in households with >2 vs ≤2 persons per bedroom]. Exposure to children aged <5 years and overcrowding were each associated with increased pneumococcal density among carriers [piaB cT difference of 2.04 (0.36–3.73) and 2.44 (0.80–4.11), respectively]. While exposure to young children was a predictor of pneumococcal carriage, associations of overcrowding with increased prevalence and density of carriage in households without young children suggest that transmission also occurs among adults in close-contact settings. IMPORTANCE Although infants and older adults are the groups most commonly affected by pneumococcal disease, outbreaks are known to occur among healthy, working-age populations exposed to overcrowding, including miners, shipyard workers, military recruits, and prisoners. Carriage of Streptococcus pneumoniae is the precursor to pneumococcal disease, and its relation to overcrowding in adult populations is poorly understood. We used molecular methods to characterize pneumococcal carriage in culture-enriched saliva samples from low-income adult farmworkers in Monterey County, CA. While exposure to children in the household was an important risk factor for pneumococcal carriage, living in an overcrowded household without young children was an independent predictor of carriage as well. Moreover, participants exposed to children or overcrowding carried pneumococci at higher density than those without such exposures, suggesting recent transmission. Our findings suggest that, in addition to transmission from young children, pneumococcal transmission may occur independently among adults in overcrowded settings.


Item
Title Page Text S1 Supplemental laboratory methods 2 Table S1 Characteristics of the primary and expanded study populations.3 Table S2 Detection of other lytA-positive oral Streptococcal carriage within the primary and expanded study populations.

4
Table S3 Detection of pneumococcal carriage among participants exposed to varying levels of household crowding, stratified according to the presence a child aged <5 years in the household.

6
Table S4 Detection of pneumococcal carriage among participants exposed to various commuting environments, stratified according to the presence of household crowding.

7
Table S5 Associations of participant characteristics with detection of other lytA-positive oral Streptococcal carriage within the primary and expanded study populations.

8
Table S6 Association of participant characteristics with lytA and piaB cT values among pneumococcal carriers.
10 Table S7 Associations of pneumococcal carriage with symptoms in last 2 weeks among study participants without SARS-CoV-2 infection.

11
Table S8 Association of symptoms with lytA and piaB cT values among study participants without SARS-CoV-2 infection.

15
Table S9 Associations of pneumococcal carriage with symptoms in last 2 weeks among all study participants.

Table S2 : Detection of other lytA-positive oral Streptococcal carriage within the primary and expanded study populations.
Table shows the prevalence of each of the exposures within the study populations stratified by carriage status.Dashes indicate variables not collected within the expanded study sample.Oral streptococcal carriage detection was defined as cT values below 40 for lytA target.

Table S5 : Associations of participant characteristics with detection of other lytA-positive oral Streptococcal carriage within the primary and expanded study populations.
Odds ratios are computed via conditional logistic regression models stratified by recruitment venue and SARS-CoV-2 infection status.

Table S6 : Association of participant characteristics with lytA and piaB cT values among pneumococcal carriers.
SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2, as detected by clinical transcription-mediated amplification testing from oropharyngeal specimens.In analyses including data from the expanded study population, there were no significant mean between-group differences in lytA cT values.Significant mean between-group differences (MD) in piaB cT values were apparent for crowded vs. uncrowded households (MD= -2.08[-3.85,-0.33];aMD-2.01[-3.86,-0.19])andhouseholdswith or without children aged <5 years (MD = -2.17).

Table S9 : Association of symptoms with lytA and piaB cT values, among SARS-CoV-2 negative participants.
Symptoms represent self-reported symptoms within the previous 2 weeks.Respiratory symptoms include dry cough, productive cough, blocked nose, runny nose, sneezing, hoarse voice, tickle in throat, sore throat, sinus pressure, difficulty breathing, wheeze, and shortness of breath.

Table S10 : Association of symptoms with lytA and piaB cT values, among all study participants.
Symptoms represent self-reported symptoms within the previous 2 weeks.Respiratory symptoms include dry cough, productive cough, blocked nose, runny nose, sneezing, hoarse voice, tickle in throat, sore throat, sinus pressure, difficulty breathing, wheeze, and shortness of breath.

Table S11 : Distribution of risk factors among participants who reported speaking Indigenous languages at home and participants who did not report speaking Indigenous languages.
are computed via Pearson's chi-squared test and Fisher's exact test.